Bioinformatics from MOURA to SHIKKAI

Shigehiko Kanaya. . . . . . . 443 [PDF]


Improvement of the quantitative differential metabolome pipeline for gas chromatography-mass spectrometry data by automated reliable peak selection

Takeshi Ara, Nozomu Sakurai, Yoshie Tange, Yoshihiko Morishita, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata. . . . . . . 445 [PDF] [Supplement 1] [Supplement 2]

We have developed a program named FAQuant that automate reliable peak selection after multiple peak alignment of gas chromatography-mass spectrometry dataset. Incorporation of this program into a pipeline of quantitative differential analysis largely reduced the total processing time.

DrEFTIR: The Data Mining Software for Fourier Transform Near-Infrared Reflectance Spectroscopy Focused on Food Metabolic Finger Printing

Tatsuhiko Ikeda, Md. Altaf-Ul-Amin, Hiroki Takahashi, Eiichiro Fukusaki. . . . . . . 451 [PDF]

We aimed at the development of the data analysis software for metabolic finger printing of food using the near-infrared spectroscopy which had very short measurement time and very wide coverage. we developed the software which could perform feature extraction and make PLS regression model.

Metabolic pathway prediction based on inclusive relation between cyclic substructures

Kenichi Tanaka, Kensuke Nakamura, Tamio Saito, Hiroyuki Osada, Aki Hirai, Hiroki Takahashi, Shigehiko Kanaya, Md.Altaf-Ul-Amin. . . . . . . 459 [PDF]

In this work, we have developed an algorithm to predict metabolic pathways on the basis of chemical structures of metabolites by exploiting the information contained in their cyclic substructures. Also, to handle a huge amount of these metabolites and to predict metabolic pathways automatically, we have developed a software tool called MetClassifier. MetClassifier is written in C and uses the OpenGL, GLUT ( and AntTweakBar ( libraries. MetClassifier can be downloaded from the following URL (

Novel bioinformatics for inter- and intraspecies comparison of genome signatures in plant genomes

Takashi Abe, Kennosuke Wada, Yuki Iwasaki, Toshimichi Ikemura. . . . . . . 469 [PDF]

For detecting species-specific sequence characteristics of each plant genome, we constructed BLSOMs for sequence fragments from one genome plus computer-generated random sequences. Genomic sequences were clearly separated from random sequences, revealing characteristics oligonucleotides including those corresponding to genetic signal sequences.

Visualization of metabolite identifier information

Fumio Matsuda, Henning Redestig, Yuji Sawada, Yoko Shinbo, Masami Yokota Hirai, Shigehiko Kanaya, Kazuki Saito. . . . . . . 479 [PDF]

A graphical representation to integrate, visualize, search, and analyze information on metabolite identifiers is demonstrated. The graphical visualization of metabolite identifier network enables us to understand the meaning of each metabolite identifier and their relationship with associated identifiers.

Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach

Atsushi Fukushima, Shigehiko Kanaya, Masanori Arita. . . . . . . 485 [PDF] [Supplement 1] [Supplement 2] [Supplement 3] [Supplement 4] [Supplement 5]

We characterized the coexpression clusters of rice genes based on unbiased graph clustering of the coexpression network, which was constructed from over 230 microarrays. The approach facilitates the generation of new testable hypotheses for the unknown functions of genes.

Predicting conformation of protein complexes by determining statistically significant domain-domain interactions

Kensaku Nishikata, Masayoshi Wada, Hiroki Takahashi, Kensuke Nakamura, Shigehiko Kanaya, Md Altaf-Ul-Amin. . . . . . . 495 [PDF] [Supplement]

The present study proposes a method to predict the configuration of protein complexes by using statistically significant domain-domain interactions (DDIs). As the first step, we extracted 312 statistically significant DDIs out of 1,162 DDIs underlying 3, 118 protein-protein interactions (PPIs) of Arabidopsis thaliana by using Fisher’s exact test. Next, 67 protein complexes were obtained by applying a graph clustering algorithm to the PPI network. Finally, we discussed the conformation of protein complexes based on DDI information extracted in the first step.

A gene co-expression database for understanding biological processes in soybean

Yoshiyuki Ogata, Hideyuki Suzuki, Daisuke Shibata. . . . . . . 503 [PDF]

We analyzed publicly available soybean gene expression datasets and developed a database for soybean gene co-expression analysis The database is useful to extract and characterize co-expressed genes for understanding biological processes.

KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants

Hiroki Takahashi, Mai Kawazoe, Masayoshi Wada, Aki Hirai, Kensuke Nakamura, Md. Altaf-Ul-Amin, Yuji Sawada, Masami Yokota Hirai, Shigehiko Kanaya. . . . . . . 509 [PDF] [Supplement 1] [Supplement 2]

We defined five-level categories concerning Arabidopsis thaliana genes by surveying approximately 3,000 references and classified 14,525 of 27,677 genes into different categories. Based on the classification information accumulated from various sources, we have developed a software tool called ‘Arabidopsis Gene Classifier'( By using this classifier system, we performed the comparative genomic analyses of five genome sequences of the plants, Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorfii, A. thaliana and Oryza sativa, and extracted statistically significant differences in their gene compositions concerning metabolic pathways.

MetalMine: a database of functional metal-ion-binding sites in proteins

Kensuke Nakamura, Aki Hirai, Md. Altaf-Ul-Amin, Hiroki Takahashi. . . . . . . 517 [PDF]

The inportance of metal-ion in protein function is well recognized. However, there has been a lack of well organized database with information concerning metalloproteins. We developed a new database called MetalMine ( In this paper, we present a brief description of this database.

Invited Review

Metabolic engineering of the tryptophan and phenylalanine biosynthetic pathways in rice

Kyo Wakasa, Atsushi Ishihara. . . . . . . 523 [PDF]

The results to modify the biosynthesis of Trp and Phe through the manipulation of key regulatory mechanisms and the effects of overproduction of these phenolic amino acids on agronomic traits, secondary metabolism, and defense reaction against pathogenic infection in plants are demonstrated.


Intergeneric hybridization among colchicaceous ornamentals, Gloriosa spp., Littonia modesta and Sandersonia aurantiaca via ovule culture

Junji Amano, Daisuke Nakazawa, Sachiko Kuwayama, Yoko Mizuta, Hajime Okuno, Yusuke Watanabe, Toshinari Godo, Dong-Sheng Han, Masaru Nakano. . . . . . . 535 [PDF]

Intergeneric hybridization was carried out among colchicaceous ornamentals, Gloriosa spp., L. modesta and S. aurantiaca. This review describes ovule culture after intergeneric cross-pollination, early confirmation of the hybridity of ovule culture-derived plantlets, and morphological characterization of some intergeneric hybrids at the flowering stage.

Original Papers

Maturation of somatic embryos as a model for soybean seed development

Keito Nishizawa, Masao Ishimoto. . . . . . . 543 [PDF]

Soybean somatic embryos have attracted attention both as a model of zygotic embryos and as explants for the generation of stable transgenic plants. We characterized the maturation of somatic embryos in detail by examining the accumulation of seed storage proteins and the changes in cellular organization, and suggested its suitability as a model of developing seeds.

Metabolic movement upon abscisic acid and salicylic acid combined treatments

Mami Okamoto, Yuuri Tsuboi, Eisuke Chikayama, Jun Kikuchi, Takashi Hirayama. . . . . . . 551 [PDF] [Supplement]

The metabolic movements in T87 Arabidopsis cultured cells induced by phytohormones were analyzed using NMR. Our results showed that co-treatment of abscisic acid and salicylic acid give a unique metabolite profile, suggesting these two hormones crosstalk not in a simple antagonistic manner but a complicate manner.

Short Communications

Stimulatory effects of sea salts on cell growth in liquid culture of Avicenniaceae mangrove

Shinji Hayashi, Shingo Kuriyama, Yoshifumi Kawana, Ai Hasegawa, Asami Kurita, Reiko Minagawa, Hamako Sasamoto. . . . . . . 561 [PDF]

Stimulatory and inhibitory effects of the seawater components, NaCl, KCl, CaCl2, MgCl2, and MgSO4, on cell growth in suspension cultures of Avicennia alba and leaf tissue of A. marina in Avicenniaceae mangroves, were investigated using a small-scale liquid culture method.

Red-purple flower due to delphinidin 3,5-diglucosides, a novel pigment for Cyclamen spp., generated by ion-beam irradiation

Emiko Kondo, Masayoshi Nakayama, Naoko Kameari, Natsu Tanikawa, Yasumasa Morita, Yusuke Akita, Yoshihiro Hase, Atsushi Tanaka, Hiroshi Ishizaka. . . . . . . 565 [PDF]

Fragrant cyclamen cultivar (C. persicum × C. purpurascens), that bloomed purple flower containing malvidin 3,5-diglucoside as the major anthocyanin, was irradiated with carbon-ion beam. Mutants were selected from M2 plants obtained by self-pollination of M1 plants. One of the mutants bloomed novel red-purple flowers, the major anthocyanin of which was delphinidin 3,5-diglucoside.